Nice improvement. Jim
On Wed, Apr 1, 2020 at 3:18 AM Rasmus Liland <[email protected]> wrote: > > On 2020-03-30 21:43 -0500, Ana Marija wrote: > > I did run your workflow and this is what I got: > > > > > newout<-merge(output11.frq,marker_info[,c("V5","match_col")],by="match_col") > > Error in `[.data.frame`(marker_info, , c("V5", "match_col")) : > > undefined columns selected > > > > this is how marker-info looks like: > > Hi Ana, > > perhaps adding comment.char="#" as an argument to read.csv might > help? > > Making the output11.frq$match_col column might perhaps be easier > using gsub, have a look: > > marker_info <- "#Column Description: > #Column is separated by ','. > #Chr: Chromosome on NCBI reference genome. > #Pos: chromosome position when snp has unique hit on reference genome. > Otherwise this field is NULL. > #Submitter_snp_name: The string identifier of snp on the platform. This > is the dbSNP local_snp_id. > #Ss#: dbSNP submitted snp Id. Each snp sequence on the platform gets a > unique ss#. > #Rs#: refSNP cluster accession. Rs# for the dbSNP refSNP cluster that the > sequence for this ss# maps to. > #Genome_build_id: Genome build used to map the SNP (a string) > #ALLELE1_genome_orient: genome orientation allele1, same as which genotypes > are reported. > #ALLELE2_genome_orient: genome orientation allele2, same as which genotypes > are reported. > #ALLELE1_orig_assay_orient: original reported orientation for the SNP > assay, will correspond to CEL files and the ss_id. > #ALLELE2_orig_assay_orient: original reported orientation for the SNP > assay, will correspond to CEL files and the ss_id. > #QC_TYPE: A-autosomal and P-pseudo-autosomal; X: X-linked; > Y-Y-linked;NA-disable QC for this snp. > #SNP_flank_sequence: snp sequence on the reference genome orientation. > 40bp on each side of variation. > #SOURCE: Platform specific string identifying assay (e.g. HBA_CHIP) > #Ss2rs_orientation: ss to rs orientation. +: same; -: opposite strand. > #Rs2genome_orienation: Orientation of rs flanking sequence to reference > genome. +: same orientation, -: opposite. > #Orien_flipped_assay_to_genome: y/n: this column would be the value of the > exclusive OR from ss2rs_orientation XOR rs2genome_orientation. > #Probe_id: NCBI probe_id. > #neighbor_snp_list: List of neighbor snp and position within 40kb > up/downstream. > #dbSNP_build_id: dbSNP build id. > #study_id: unique id with prefix: phs. > # > # > Chr,Pos,Submitter_snp_name,Ss#,Rs#,Genome_build_id,ALLELE1_genome_orient,ALLELE2_genome_orient,ALLELE1_orig_assay_orient,ALLELE2_orig_assay_orient,QC_TYPE,SNP_flank_sequence,SOURCE,Ss2rs_orientation,Rs2genome_orienation,Orien_flipped_assay_to_genome,Probe_id,neighbor_snp_list,dbSNP_build_id,study_id > 1,742429,SNP_A-1909444,ss66079302,rs3094315,36.2,G,A,C,T,A,GCACAGCAAGAGAAAC[A/G]TTTGACAGAGAATACA,Sty,+,-,y,,,127,phs000018 > 1,769185,SNP_A-4303947,ss66273559,rs4040617,36.2,A,G,A,G,A,GCTGTGAGAGAGAACA[A/G]TGTCCCAATTTTGCCC,Sty,+,+,n,,,127,phs000018 > 1,775852,SNP_A-1886933,ss66317030,rs2980300,36.2,T,C,A,G,A,GAATGACTGTGTCTCT[C/T]TGAGTTAGTGAAGTCA,Nsp,-,+,y,,,127,phs000018 > " > marker_info <- > read.csv(text=marker_info, > header=FALSE, > stringsAsFactors=FALSE, > comment.char="#") > > output11.frq <- > "CHR SNP A1 A2 MAF NCHROBS > 1 1:775852:T:C T C 0.1707 3444 > 1 1:1120590:A:C C A 0.08753 3496 > 1 1:1145994:T:C C T 0.1765 3496 > 1 1:1148494:A:G A G 0.1059 3464 > 1 1:1201155:C:T T C 0.07923 3496" > output11.frq <- > read.table(text=output11.frq, header=TRUE, > stringsAsFactors=FALSE) > > output11.frq$match_col <- > gsub("^([0-9]+):([0-9]+).*", "\\1:\\2", > output11.frq$SNP) > > marker_info$match_col <- > apply(marker_info[,1:2], 1, paste, > collapse=":") > > merge(x=output11.frq, > y=marker_info[,c("V5", "match_col")], > by="match_col") > > > Regards, > Rasmus > > ______________________________________________ > [email protected] mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
